Mr. Abaaoud was identified with fingerprints taken from his body at the scene of Wednesday’s raid by police on an apartment north of Paris, the prosecutor said.
The militant’s death marks a coup for French authorities who tracked Mr. Abaaoud to a house in the Paris suburb of Saint-Denis using witness tips. French SWAT teams battled with Mr. Abaaoud and others with suspected terrorist links for hours on Wednesday, firing 5,000 rounds to subdue the group holed up in an apartment.
French Interior Minister Bernard Cazeneuve said Mr. Abaaoud was implicated in four out of six terror plots French authorities have prevented in recent months.
The Belgian-born operative is suspected of having planned and coordinated three teams of attackers who carried out the brazen assaults on the French capital on Friday, using explosives and automatic rifles to kill 129 people.
“The brain or one of the brains—we have to be extremely careful—was found among the dead,” French Prime Minister Manuel Valls told parliament on Thursday. The prime minister praised the police for tracking down the militant.
President François Hollande convened a meeting later Thursday with senior members of his government, including the defense and interior ministers. France’s National Assembly approved a bill expanding the government’s emergency powers to conduct searches and confine residents, the first step in a series of sweeping proposals from Mr. Hollande.
French authorities worked through the night to identify Mr. Abaaoud’s remains, which were badly damaged in the chaos of the raid. One woman wearing explosives blew herself up as police stormed the building, prosecutors said, bringing down the ceiling.
Mr. Abbaaoud was implicated in an attempt to attack churches in April that ended with the detention of Sid Ahmed Ghlam, who is suspected of killing a woman as he allegedly prepared to strike, Mr. Cazeneuve said. French authorities are also looking into whether Mr. Abbaaoud was involved in preparing the attacks on the Amsterdam-Paris Thalys train in August, which were foiled by passengers who wrestled assailants to the ground.
French authorities had sought to neutralize the Islamic operative, who had been believed to be in Syria, for months, including by mounting failed attempts to kill him through airstrikes.
The repeated appearance of Mr. Abaaoud on French intelligence radar and his apparent ability to slip through borders unchecked raised concerns about the continent’s security.
No European country had flagged the presence of the suspected terrorist in the region, Mr. Cazeneuve said. Only on Monday—three days after the Paris attacks—did intelligence services outside of Europe inform France they had tracked Mr. Abaaoud’s recent movements in Greece, he said, though he didn’t elaborate further.
Mr. Cazeneuve defended France’s security services and called for the continent to do more to crack down on terrorism, including better tracking travelers, strengthening borders, and coordinating efforts to clamp down on arms trafficking.
“All that isn’t going fast enough, it’s not going far enough,” he said
As France hunted for Mr. Abaaoud, investigators tried to piece together his record, a career that stretches from the suburbs of Brussels to the killing fields of Syria.
The Belgian was a military commander, or “emir of war,” in Syria’s eastern Deir Ezzour province, according to local activists and news reports, an unusually high rank for fighter from Europe. Friends from his early life in Brussels, in the predominantly Muslim district of Molenbeek, recall a “nice guy” who played soccer.
Long before the Paris onslaught, he guided militants, including a French national and former Islamic State jailer who returned to Europe to launch a May 2014 assault rifle attack on the Jewish Museum of Belgium, killing four.
Little has been known about Mr. Abaaoud’s criminal record. In an interview on Thursday, the operative’s lawyer Alexandre Chateau said he had been repeatedly arrested for violent crimes around Brussels and served time in at least three prisons.
In December 2010, Mr. Abaaoud and Salah Abdeslam, who allegedly drove militants during Friday’s attack and escaped, were convicted on charges unrelated to terrorism in the same case and sent to prison.
Mr. Chateau said Mr. Abaaoud was arrested for attempting to break into a parking garage with Mr. Abdeslam.
Mr. Chateau said he became his lawyer in 2006 when he was arrested for theft. The last time he saw him in 2013, he had grown out his beard and become a more observant Muslim, Mr. Chateau said.
“He didn’t show signs of radicalization or that he would be implicated in terrorist acts or that he would fight overseas,” Mr. Chateau said.
Mr. Abaaoud’s family came from Morocco and owned a clothing store in Molenbeek. Until 2013, Mr. Abaaoud was closely associated with the business. He was its largest shareholder in 2013 and presided over board meetings, according to corporate records.
At the start of 2014, he headed for Syria where he was assigned to menial tasks by Islamic State but he quickly rose through the ranks to successes in military operations in Syria and Iraq, according to fighters and activists.
Western officials said he was eventually assigned the bigger role of organizing attack missions in Europe.